BSDB

The conformational change and the identification of the mechanical clamp for proteins can be derived by looking at the unfolding scenario. A unfolding scenario shows distance d_u at which a given native contact is broken for the last time. Contacts in the scenario diagrams are identified by the sequential distance |j - i|. A contact is said to be broken if the distance between amino acids i and j exceeds 1.5σ_ij. An accumulation of many contacts unfolding events at a value of d_u indicates emergence of a force peak. In such figure the y-axis shows the sequential separation between two amino acids that make a native contact. The x-axis indicates at which displacement of the pulling tip the contact is broken for the last time. Notice that thermal fluctuations may reinstate a broken contact temporarily and that’s why we seek the last, and thus definitive, rupture event.

As an example we show the unfolding diagram for the first chain of protein 1c4p. This protein contains an α helix (196-210), denoted as I, and eight β strands, denoted as A through H, as labelled consecutively from the N to C termini. These β strands form three β sheets: a, b, and c. The a sheet comprises four strands (A, B, G, E), b sheet two ( C, F), and c-sheet also two ( D, H). These letters are indicated on the unfolding scenario figure and show which secondary structures are involved in a contact that is broken at the distance d_u. The data symbols marked by asterisks correspond to contacts which do not involve any secondary structures. The remaining symbols are diversified and have a meaning identified by the letter symbols placed next to them. The force peak at about 140 Å involves a near simultaneous rupture of the contacts which relate to the terminal strands A and G: A+G (meaning between A and G), A+I, G+I (i.e. with the helix) as well as D+H, A+B, E+G, D+G, C+G, and A+C. Breaking these contacts results in destroying the a β-sheet. Later on, the remaining contacts, such as C+F in the b sheet are broken and the helix is the last to unravel.

ICN I J |I-J| Displacement error 1 2 7 5 439.81 0.62 2 2 73 71 31.74 0.14 3 2 76 74 28.80 1.07 4 2 127 125 21.84 0.40 5 2 128 126 21.80 0.38 6 3 6 3 474.34 0.29 7 3 7 4 462.26 5.75 8 4 7 3 474.00 0.12 9 4 8 4 462.35 5.70 10 5 8 3 477.05 1.54 11 5 9 4 474.43 0.34 12 6 9 3 477.72 1.21 13 6 10 4 462.52 6.30 14 6 124 118 47.83 0.52 15 6 127 121 47.85 0.51 16 7 10 3 477.05 1.54 17 7 11 4 469.20 2.96 18 7 73 66 48.66 0.64 19 7 74 67 49.25 0.35 20 8 11 3 474.67 0.43 21 8 12 4 469.22 2.95 22 9 12 3 477.05 0.10 23 9 13 4 469.19 2.94 24 9 121 112 63.22 0.29 25 9 124 115 63.16 0.27 26 10 13 3 478.88 1.02 27 10 14 4 469.13 2.94 28 10 70 60 63.22 0.29 29 10 124 114 63.22 0.29 30 10 125 115 63.16 0.27 31 10 128 118 63.15 0.27 32 11 14 3 477.96 1.48 33 11 15 4 463.80 5.59 34 11 70 59 63.30 0.27 35 11 71 60 63.32 0.28 36 11 73 62 63.30 0.28 37 12 15 3 469.56 1.82 38 12 16 4 469.56 1.82 39 13 16 3 477.82 1.42 40 13 17 4 469.56 1.82 41 13 113 100 82.78 0.71 42 13 121 108 63.58 0.18 43 13 125 112 63.38 0.27 44 14 17 3 469.56 1.81 45 14 18 4 465.03 0.46 46 14 21 7 410.39 0.12 47 14 66 52 63.35 0.27 48 14 67 53 63.38 0.26 49 14 70 56 63.37 0.26 50 14 109 95 79.12 0.75 51 15 18 3 466.62 1.25 52 16 113 97 95.55 1.51 53 16 116 100 93.95 0.71 54 17 20 3 474.87 0.26 55 17 21 4 437.30 8.03 56 17 24 7 416.92 2.17 57 17 109 92 91.32 0.61 58 17 113 96 96.65 1.17 59 18 21 3 493.20 3.39 60 20 23 3 475.54 2.06 61 20 24 4 469.02 0.10 62 21 24 3 472.41 1.57 63 21 25 4 464.12 2.56 64 21 63 42 103.41 1.03 65 22 25 3 468.12 0.57 66 22 26 4 464.13 2.56 67 22 59 37 108.95 0.35 68 22 60 38 104.31 0.61 69 22 63 41 103.47 1.01 70 23 26 3 481.50 4.88 71 23 27 4 464.11 2.56 72 23 56 33 118.01 0.16 73 24 27 3 481.81 4.73 74 24 28 4 463.01 2.34 75 24 108 84 118.08 0.15 76 24 109 85 118.56 0.40 77 24 112 88 127.98 0.24 78 25 28 3 471.04 1.68 79 25 29 4 468.64 2.87 80 25 59 34 118.00 0.17 81 25 63 38 117.94 0.16 82 26 29 3 469.91 2.23 83 26 30 4 465.37 1.22 84 26 55 29 125.63 1.60 85 26 56 30 126.91 0.89 86 26 59 33 120.33 1.03 87 27 30 3 470.14 1.17 88 27 31 4 465.35 1.23 89 27 108 81 128.93 0.06 90 27 112 85 129.56 0.14 91 28 31 3 475.10 1.31 92 28 32 4 465.36 1.23 93 28 101 73 128.50 0.21 94 28 104 76 128.53 0.23 95 28 105 77 128.46 0.22 96 28 108 80 128.96 0.07 97 29 32 3 475.45 1.03 98 29 33 4 464.66 1.58 99 29 55 26 129.48 0.07 100 29 58 29 128.87 0.19 101 29 59 30 128.69 0.24 102 29 101 72 128.60 0.21 103 30 33 3 484.35 1.05 104 30 34 4 462.98 0.74 105 30 50 20 129.63 0.12 106 31 34 3 482.74 1.86 107 31 35 4 461.66 1.35 108 31 104 73 129.10 0.02 109 31 107 76 129.43 0.12 110 31 108 77 129.45 0.13 111 32 35 3 473.35 0.02 112 32 36 4 451.80 3.56 113 32 39 7 252.53 27.84 114 32 100 68 129.10 0.02 115 32 101 69 129.03 0.01 116 32 104 72 129.38 0.12 117 33 37 4 417.74 5.23 118 33 39 6 304.57 1.81 119 33 40 7 168.19 0.30 120 33 43 10 161.77 0.43 121 33 48 15 129.75 0.09 122 34 37 3 482.88 0.90 123 36 39 3 485.61 3.94 124 36 100 64 129.11 0.02 125 36 103 67 129.59 0.10 126 36 104 68 129.62 0.12 127 37 40 3 480.00 0.09 128 38 41 3 482.82 0.68 129 39 42 3 484.31 0.10 130 39 100 61 129.46 0.11 131 40 43 3 494.28 1.80 132 40 44 4 475.10 0.52 133 40 48 8 137.25 2.11 134 41 44 3 494.37 1.76 135 42 93 51 128.97 0.08 136 42 94 52 129.19 0.03 137 42 97 55 129.50 0.10 138 43 46 3 477.69 1.11 139 43 48 5 423.62 6.67 140 43 58 15 131.34 0.04 141 45 54 9 139.60 3.01 142 46 54 8 139.56 3.03 143 46 58 12 137.49 2.00 144 47 52 5 231.39 37.87 145 47 54 7 139.62 3.02 146 47 55 8 139.62 3.02 147 48 52 4 385.77 6.80 148 48 55 7 139.62 3.01 149 49 52 3 475.97 0.88 150 52 55 3 473.57 1.06 151 52 56 4 470.25 2.56 152 53 56 3 470.25 2.56 153 53 57 4 468.39 3.50 154 54 57 3 476.17 5.12 155 54 58 4 464.03 2.77 156 55 58 3 472.47 1.45 157 55 59 4 461.68 3.95 158 56 59 3 473.63 2.03 159 56 60 4 462.07 3.74 160 57 60 3 479.91 1.21 161 57 61 4 471.06 0.76 162 58 61 3 471.06 0.76 163 58 62 4 471.08 0.77 164 59 62 3 473.60 0.29 165 59 63 4 471.08 0.78 166 60 63 3 473.59 2.03 167 60 64 4 470.44 1.09 168 61 64 3 471.36 1.57 169 61 65 4 472.62 0.01 170 62 65 3 483.15 0.40 171 62 66 4 470.34 1.15 172 63 66 3 478.30 2.83 173 63 67 4 464.66 1.70 174 64 67 3 470.35 1.15 175 64 68 4 464.98 1.55 176 65 68 3 470.36 1.14 177 65 69 4 464.99 1.55 178 65 83 18 149.19 0.20 179 66 69 3 478.31 2.04 180 66 70 4 464.99 1.55 181 66 105 39 162.47 1.65 182 66 128 62 169.06 3.98 183 66 129 63 157.94 0.27 184 66 132 66 157.56 0.32 185 67 70 3 475.34 1.32 186 67 71 4 470.39 1.14 187 68 71 3 475.07 1.19 188 68 72 4 470.40 1.14 189 68 79 11 158.50 0.10 190 69 72 3 475.41 1.36 191 69 73 4 459.56 6.55 192 69 76 7 222.09 26.67 193 69 80 11 158.41 0.05 194 69 128 59 174.40 1.31 195 69 132 63 161.75 1.61 196 70 73 3 467.87 2.41 197 70 128 58 183.09 2.96 198 72 75 3 471.42 0.29 199 72 76 4 449.82 10.51 200 72 79 7 281.61 0.59 201 73 76 3 477.25 2.62 202 75 78 3 480.41 1.73 203 75 79 4 470.05 0.64 204 76 79 3 470.03 0.63 205 76 80 4 465.37 1.70 206 76 128 52 269.45 0.10 207 76 132 56 259.61 2.15 208 77 80 3 472.18 0.32 209 77 81 4 467.54 0.60 210 77 135 58 258.98 2.46 211 78 81 3 469.17 1.42 212 80 83 3 479.44 0.58 213 80 84 4 462.19 0.84 214 80 132 52 271.36 0.94 215 80 135 55 271.74 1.15 216 80 136 56 271.74 1.16 217 81 84 3 474.25 3.17 218 81 85 4 462.23 0.83 219 81 139 58 271.77 1.17 220 82 85 3 480.49 1.10 221 82 86 4 471.10 2.37 222 83 86 3 485.62 1.86 223 83 87 4 475.68 4.66 224 83 136 53 271.95 1.24 225 84 87 3 483.85 0.58 226 84 88 4 463.01 0.46 227 84 135 51 272.00 1.22 228 84 136 52 271.94 1.25 229 84 138 54 271.93 1.24 230 84 139 55 271.91 1.25 231 85 88 3 483.45 0.78 232 85 89 4 460.57 0.77 233 85 139 54 271.93 1.24 234 86 89 3 485.32 0.17 235 86 90 4 435.28 2.12 236 86 91 5 433.87 1.40 237 87 91 4 433.87 1.40 238 87 92 5 387.74 7.41 239 87 93 6 374.14 14.21 240 87 98 11 300.87 13.04 241 87 136 49 272.00 1.22 242 87 140 53 271.92 1.24 243 88 92 4 374.16 14.20 244 88 139 51 271.94 1.24 245 88 140 52 271.88 1.22 246 89 92 3 492.91 3.16 247 92 140 48 272.01 1.22 248 93 97 4 479.93 0.98 249 93 98 5 471.96 2.14 250 93 140 47 272.05 1.22 251 94 97 3 484.87 0.86 252 94 98 4 484.61 0.99 253 95 98 3 483.05 0.21 254 95 140 45 272.17 1.20 255 96 99 3 480.88 0.49 256 96 100 4 478.06 0.92 257 97 100 3 480.94 0.53 258 97 101 4 475.23 1.02 259 98 101 3 477.81 2.38 260 98 102 4 470.30 1.37 261 98 133 35 272.31 1.15 262 98 136 38 272.63 1.28 263 98 140 42 272.36 1.17 264 99 102 3 476.72 1.84 265 99 103 4 470.26 1.39 266 100 103 3 476.71 1.84 267 100 104 4 473.29 1.35 268 101 104 3 476.10 0.05 269 101 105 4 465.63 0.27 270 102 105 3 475.88 0.07 271 102 106 4 464.16 0.48 272 102 129 27 273.14 1.07 273 102 133 31 272.75 1.25 274 103 106 3 471.94 0.84 275 103 107 4 463.80 0.67 276 104 107 3 466.56 2.04 277 104 108 4 466.56 2.04 278 105 108 3 471.62 2.77 279 105 109 4 463.84 0.65 280 105 129 24 274.32 1.34 281 106 109 3 472.72 2.39 282 106 110 4 464.11 0.70 283 106 117 11 275.00 1.38 284 106 122 16 274.38 1.34 285 106 125 19 274.38 1.34 286 106 126 20 274.34 1.34 287 106 129 23 274.33 1.33 288 107 110 3 472.12 2.38 289 107 111 4 466.38 0.43 290 108 111 3 474.69 3.66 291 108 112 4 474.62 3.70 292 109 112 3 482.75 0.37 293 109 113 4 458.01 2.33 294 109 125 16 274.83 1.38 295 110 113 3 479.81 1.83 296 110 117 7 275.09 1.34 297 113 116 3 477.86 0.55 298 113 117 4 361.58 6.80 299 115 118 3 526.28 0.91 300 116 121 5 463.89 3.71 301 117 121 4 465.24 3.04 302 117 122 5 463.89 3.71 303 117 125 8 408.91 8.03 304 118 121 3 468.31 1.51 305 118 122 4 468.31 1.51 306 119 122 3 468.32 1.51 307 119 123 4 468.31 1.51 308 120 123 3 475.25 1.96 309 120 124 4 468.32 1.51 310 121 124 3 474.73 1.70 311 121 125 4 461.33 1.98 312 122 125 3 474.87 1.77 313 122 126 4 461.25 2.02 314 123 126 3 474.94 1.72 315 123 127 4 461.47 1.91 316 124 127 3 474.55 1.80 317 124 128 4 465.85 0.29 318 125 128 3 472.36 3.54 319 125 129 4 467.89 0.73 320 126 129 3 482.05 1.31 321 126 130 4 467.89 0.73 322 127 130 3 481.29 0.93 323 127 131 4 464.67 1.72 324 128 131 3 475.13 4.01 325 128 132 4 464.78 1.66 326 129 132 3 475.88 3.64 327 129 133 4 461.35 0.05 328 130 133 3 463.53 1.15 329 130 134 4 461.25 0.01 330 131 134 3 467.79 0.98 331 131 135 4 461.11 0.09 332 132 135 3 474.12 5.26 333 132 136 4 464.15 1.51 334 133 136 3 476.43 4.11 335 133 137 4 463.90 0.15 336 134 137 3 479.28 2.38 337 134 138 4 460.04 0.78 338 135 138 3 479.28 2.38 339 136 140 4 491.44 0.39 340 137 140 3 485.50 0.97